The fabrication of semiconductor devices, such as logic and memory devices, typically includes processing a substrate such as a semiconductor wafer using a large number of semiconductor fabrication processes to form various features and multiple levels of the semiconductor devices. As semiconductor device size becomes smaller and smaller, it becomes critical to develop enhanced inspection and review devices and procedures. One such inspection technology includes electron beam based inspection systems, such as, scanning electron microscopy (SEM). Single beam SEM systems may image a surface of a sample through the collection and analysis of electrons emitted or scattered from the surface of the sample as a primary beam is scanned across the sample. In single beam SEM systems, it is generally difficult to separate noise from image information. This difficulty arises due to the fact that i) it is difficult to be certain that an image artifact is noise and not an actual image feature; and ii) there may not be enough feature information (such as straight sharp edges) in a single image to extract noise. With the implementation of multi-beam SEM systems, inspection times have reduced dramatically due to the simultaneous acquisition of image data from multiple regions of a sample, however noise mitigation techniques in multi-beam SEM systems have proven ineffective. Therefore, it would be advantageous to provide a system and method that reduces or mitigates noise in a multi-beam SEM system.